Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
Open accessAbstract
The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell type would be transformative for understanding systems-level properties as well as specific pathways in physiology and disease. Here, we describe the generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins by the widely accessible, sensitive, and robust targeted mass spectrometric method selected reaction monitoring, SRM. This human SRMAtlas provides definitive coordinates that conclusively identify the respective peptide in biological samples. We report data on 166,174 proteotypic peptides providing multiple, independent assays to quantify any human protein and numerous spliced variants, non-synonymous mutations, and post-translational modifications. The data are freely accessible as a resource at http://www.srmatlas.org/, and we demonstrate its utility by examining the network response to inhibition of cholesterol synthesis in liver cells and to docetaxel in prostate cancer lines.
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The Human SRMAtlas assay library enables targeted identification and quantification of a theoretical maximum of 99.7% of the human proteome, provided proteins are expressed spatiotemporally at concentrations amenable to MS detection.
“This assay library enables targeted identification and quantification of a theoretical maximum of 99.7% of the human proteome36, provided proteins are expressed spatiotemporally at concentrations amenable to MS detection.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [36]
In silico analysis reveals only 22 human proteins cannot produce the characteristic >2 high-stringency proteotypic peptides of the required length after tryptic digestion.
“In silico analysis reveals only 22 human proteins cannot produce the characteristic >2 high-stringency proteotypic peptides of the required length after tryptic digestion36.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [36]
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References 39 · Cited by 310
- Authors
- Kusebauch, U., Campbell, D. S., Deutsch, E. W., Chu, C. S., Spicer, D. A., Brusniak, M.-Y., Slagel, J., Sun, Z., Stevens, J., Grimes, B., Shteynberg, D., Hoopmann, M. R., Blattmann, P., Ratushny, A. V., Rinner, O., Picotti, P., Carapito, C., Huang, C.-Y., Kapousouz, M., Lam, H., Tran, T., Demir, E., Aitchison, J. D., Sander, C., Hood, L., Aebersold, R., & Moritz, R. L.
- Affiliations
- Institute for Systems Biology (US)
- ETH Zurich (CH)
- Center for Infectious Disease Research (US)
- Hong Kong University of Science and Technology (HK)
- Memorial Sloan Kettering Cancer Center (US)
- University of Zurich (CH)
- Corresponding author
- Aebersold, Ruedi
- Moritz, Robert L.
- ORCID
- Kusebauch, Ulrike
- Campbell, David S.
- Deutsch, Eric W.
- Brusniak, Mi-Youn
- Slagel, Joseph
- Sun, Zhi
- Grimes, Barbara
- Shteynberg, David
- Hoopmann, Michael R.
- Blattmann, Peter
- Ratushny, Alexander V.
- Picotti, Paola
- Carapito, Christine
- Lam, Henry
- Demir, Emek
- Aitchison, John D.
- Sander, Chris
- Hood, Leroy
- Aebersold, Ruedi
- Moritz, Robert L.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2016-07
- Volume
- 166
- Issue
- 3
- Pages
- 766-778
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC5245710
- OpenAlex
- W2488048472
- Cited by
- 310
- References
- 39
- Citations by year
- 2026: 3 · 2025: 11 · 2024: 21 · 2023: 15 · 2022: 24 · 2021: 27 · 2020: 31 · 2019: 44 · 2018: 48 · 2017: 62 · 2016: 24
- FWCI
- 29.55
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (130530)
- National Human Genome Research Institute (RC2HG005805, U41HG006623)
- National Institute of General Medical Sciences (P41GM109824, R01GM087221, P50GM076547)
- National Center for Research Resources (S10RR027584)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- human proteome, multiple reaction monitoring, targeted proteomics, proteotypic peptides, protein quantification, splice variants, non-synonymous mutations, post-translational modification, cholesterol synthesis inhibition, docetaxel, prostate cancer, hepatocytes
- MeSH terms
- Docetaxel, Antineoplastic Agents, Cholesterol, Female, Humans, Liver, Male, Mutation, Prostatic Neoplasms, RNA Splicing, Internet, Proteome, Access to Information, Databases, Protein, Taxoids, Cell Line, Tumor
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